typically I am using full DE Nextflow pipeline that as an input takes fastq files.
However now I want to compare my data with other people experiments from NCBI SRA. Unfortunately I have data in BAM format. I know that I could convert it back to fastq however it would be super inefficient for over 400 files.
Does anybody knows any Nextflow/Snakemake pipelines that accepts BAMs for DE DEseq2 analysis?
Thank you for any tips!